|
| Status |
Public on Jul 09, 2024 |
| Title |
Patient 3 at (T0) |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral Blood Mononuclear Cells (PBMCs) before surgery
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
age: 46
type of surgery: Biliopacreatic Diversion without duodenal switch
phenotype: Responder
tissue: PBMCs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted from PBMCs using the SV Total RNA Isolation Kit from Promega following the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
500 ng of total RNA were used to synthesis cDNA and preparing biotinylated cRNA according to the Affymetrix protocol
|
| |
|
| Hybridization protocol |
11 µg of labeled and fragmented cRNA were hybridized for 16 hours at 54 C on Affymetrix Human Genome U133 Plus 2.0 Array. After that, washing and staining of the GeneChips were performed using the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from obese patient before the bariatric surgery
|
| Data processing |
We processed the raw CEL files using freely available updated chip definition files (CDF) for HG-U 133 Plus 2.0 arrays based on Entrez genes, which remaps every probe in the array, re-aligning to the sequences of the latest genome assembly. Specifically, we used three libraries of version 22, namely HG-U 133 Plus 2.0 Entrez gcdf, HG-U 133 Plus 2.0 Entrez gprobe, and HG-U 133 Plus 2.0 Entrez gdb (2) from http://mbni.org/customcdf/22.0.0. We imported and converted the probe intensity data from the CEL files along with the above-mentioned CDF file into the probe level ‘AffyBatch’ object by ReadAffy function of the Affy R package in Bioconductor (3). We imported the phenotypic data using the pData function into the AffyBatch object. Finally, we used (4)the RMA function on this object for background correction, normalization of the multiple array data using the Robust Multiarray Average (RMA) method, and expression calculation for the entire probes available in the CDF file. This step produces an object containing probe level expression matrix. We populated the probe level feature data into this ‘Expression Set’ object using annotateEset function of the R package ‘affycoretools’ and chipDB object (hgu133plus2hsrefseq.db) from the brain array project. Then, we used the ‘exprs’ function in the Affy package to extract the expression matrix of the genes / probes for further downstream analyzes.
|
| |
|
| Submission date |
Jul 08, 2024 |
| Last update date |
Jul 09, 2024 |
| Contact name |
Abderrezak Bouchama |
| E-mail(s) |
rezakbouchama@gmail.com
|
| Organization name |
KAIMRC
|
| Department |
Experimental Medicine
|
| Street address |
Ahmad Ibn Hanbal Street, Ar Rimayah
|
| City |
Riyadh |
| ZIP/Postal code |
11481 |
| Country |
Saudi Arabia |
| |
|
| Platform ID |
GPL34684 |
| Series (1) |
| GSE271700 |
Transcriptome Changes and Metabolic Outcomes After Bariatric Surgery in Adults With Obesity and Type 2 Diabetes |
|
